Nature Biotechnology Contents: Volume 31 pp 263 - 364

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Apply online today or call 919-405-2248 * 866-293-6094 Subscribe   Facebook   RSS   Recommend to library   Twitter   Advertisement BIOPHARMA DEALMAKERS Company Profiles and Partnering Opportunities   Advertisement Nature Publishing Group and Relay Technology Management present: The Epigenetics Target Explorer Click here to access this free online tool and the accompanying article in Nature Reviews Drug Discovery.   Focus Top Focus on translating the microbiome Researchers have generated more than 3.5 terabytes of human microbiome genomic information - more than 1,000 times that generated by the Human Genome Project. This Focus highlights progress in microbiome research and how these data might translate into a better understanding of human diseases and rational design of new therapies. Table of Contents In This Issue Top In this issue   ppvii - vii doi:10.1038/nbt.2562 Editorials Top Laying better plans for mice   p263 doi:10.1038/nbt.2560 Genetically defined germ-free animal models colonized with defined microbiota are crucial for progress in microbiome research. Building a wall against biosimilars   p264 doi:10.1038/nbt.2550 The brand biotech industry is erecting barriers to biosimilars that will slow market entry and torpedo price competition. News Top Companies 'going long' generate sequencing buzz at Marco Island   pp265 - 266 Michael Eisenstein doi:10.1038/nbt0413-265 FDA dashes Novo's hopes   p266 Emma Dorey doi:10.1038/nbt0413-266 Mouse platforms jostle for slice of humanized antibody market   pp267 - 268 Nuala Moran doi:10.1038/nbt0413-267 Farmer threat to Monsanto recedes   p268 Michael Francisco doi:10.1038/nbt0413-268 Biosimilars battle rages on, Amgen fights both sides   pp269 - 270 Melanie Senior doi:10.1038/nbt0413-269 Three deaths sink Affymax   p270 Laura DeFrancesco doi:10.1038/nbt0413-270a Monsanto buys microbes   p270 Emily Waltz doi:10.1038/nbt0413-270b Sequestration to slash research grants and delay biosimilars   p271 Jeffrey L Fox doi:10.1038/nbt0413-271 Canadian visas woo entrepreneurs   p272 Stephen Strauss doi:10.1038/nbt0413-272a Spain nudges biotech from nest   p272 Lucas Laursen doi:10.1038/nbt0413-272b Japan punts on regenerative medicine   pp272 - 273 David Cyranoski doi:10.1038/nbt0413-272c Around the world in a month   p273 doi:10.1038/nbt0413-273 Urea cycle disorder drug approved   p274 Malini Guha doi:10.1038/nbt0413-274 Alliance to bolster translation of academic R&D assets   p275 Malorye Allison doi:10.1038/nbt0413-275 Data Page Trends in microbiome research   p277 Susan Jones doi:10.1038/nbt.2546 Brazil, Canada and South Africa bullish on agbiotech   p278 Andrew Marshall doi:10.1038/nbt.2552 News Features The startup bugs   pp279 - 281 Charles Schmidt doi:10.1038/nbt.2544 Burgeoning research on the human microbiome is facilitating the development of more mechanistically driven probiotics. Charles Schmidt investigates a smattering of probiotic- and microbiota-modifying therapeutic opportunities arising from commercial efforts. A snapshot of the microbiome field   pp282 - 283 Susan Jones doi:10.1038/nbt.2545 A survey of leading scientists from academia and industry highlights notable papers that have garnered momentum in microbiome research. Bioentrepreneur Top Building a business Building for big pharma   pp284 - 287 Asiya Giniatullina, Marco Boorsma, Geert-Jan Mulder and Sander van Deventer doi:10.1038/nbt.2533 SciCafé Startups on the Menu: EnBiotix   p287 doi:10.1038/nbt0413-287 Opinion and Comment Top Correspondence Correcting misperceptions about cryopreserved embryos and stem cell research   pp288 - 290 Geoffrey P Lomax and Alan O Trounson doi:10.1038/nbt.2541 ProtoNet: charting the expanding universe of protein sequences   pp290 - 292 Nadav Rappoport, Nathan Linial and Michal Linial doi:10.1038/nbt.2553 Alternative splicing and protein interaction data sets   pp292 - 293 David Talavera, David L Robertson and Simon C Lovell doi:10.1038/nbt.2540 Updating benchtop sequencing performance comparison   pp294 - 296 Sebastian Junemann, Fritz Joachim Sedlazeck, Karola Prior, Andreas Albersmeier, Uwe John, Jorn Kalinowski, Alexander Mellmann, Alexander Goesmann, Arndt von Haeseler, Jens Stoye and Dag Harmsen doi:10.1038/nbt.2522 Reply to Updating benchtop sequencing performance comparison   p296 Mark John Pallen doi:10.1038/nbt.2531 Commentary Metcalfe's law and the biology information commons   pp297 - 303 Stephen H Friend and Thea C Norman doi:10.1038/nbt.2555 Open collaboration on biomedical discoveries requires a fundamental shift in the traditional roles and rewards for both investigators and participants in research. Features Top Translating the human microbiome   pp304 - 308 James Brown, Willem M de Vos, Peter S DiStefano, Joel Dore, Curtis Huttenhower, Rob Knight, Trevor D Lawley, Jeroen Raes and Peter Turnbaugh doi:10.1038/nbt.2543 Nine experts discuss the challenges in translating current research on the human microbiome into strategies for disease prediction, diagnosis and therapy. Medicines from microbiota   pp309 - 315 Bernat Olle doi:10.1038/nbt.2548 Five years after the launch of the Human Microbiome Project, several ventures are seeking to capitalize on the clinical promise of microbiome modulation. Commercialization of drugs that influence the human flora poses some unique scientific, translational and regulatory challenges. Patents Federal Trade Commission v. Actavis, Inc. and reverse-payment or pay-for-delay settlements   pp316 - 317 Jacob S Sherkow doi:10.1038/nbt.2542 An imminent US Supreme Court ruling should resolve one of the thorniest legal issues facing pharmaceutical companies today. Recent patent applications in bacteriotherapy   p318 doi:10.1038/nbt.2559 News and Views Top Renewable RNAi   pp319 - 320 James A Blau and Michael T McManus doi:10.1038/nbt.2547 siRNAs for knocking down target genes in mammalian cells can now be made in bacteria. See also: Research by Huang et al. Compartmentalizing metabolic pathways in organelles   pp320 - 321 William C DeLoache and John E Dueber doi:10.1038/nbt.2549 The entire metabolic pathway for producing a biofuel is confined within a yeast organelle to increase yield over the endogenous pathway split between two compartments. See also: Research by Avalos et al. Targeting autophagy for disease therapy   pp322 - 323 Kurt M Lucin and Tony Wyss-Coray doi:10.1038/nbt.2554 A peptide that enhances autophagy suppresses viral infections and clears protein aggregates. Research Highlights   p323 doi:10.1038/nbt.2557 Biotechnology JOBS of the week Group Leader Postion in Bioinformatics The Institute of Genetic Diseases Imagine Faculty Positions in Computational Biology and Bioinformatics The Geroge Washington University Postdoctoral Research Fellow (Bioinformatics) Icahn School of Medicine at Mount Sinai Postdoc Bioinformatics (m / f) Bayer CropScience AG Postdoctoral Fellow Mount Sinai School of Medicine (Brown Lab) More Science jobs from Biotechnology EVENT Plant Genomes & Biotechnology: from genes to networks July 12, 2013 Cold Spring Harbor, US More science events from Computational Biology Top Analysis Mutation identification by direct comparison of whole-genome sequencing data from mutant and wild-type individuals using k-mers   pp325 - 330 Karl J V Nordstrom, Maria C Albani, Geo Velikkakam James, Caroline Gutjahr, Benjamin Hartwig, Franziska Turck, Uta Paszkowski, George Coupland and Korbinian Schneeberger doi:10.1038/nbt.2515 Genes that cause a mutant phenotype are efficiently identified from genetic screens of model and non-model organisms from whole-genome sequencing data without requiring segregating populations, genetic maps and reference sequences. Research Top Brief Communications Protein interaction discovery using parallel analysis of translated ORFs (PLATO)   pp331 - 334 Jian Zhu, H Benjamin Larman, Geng Gao, Romel Somwar, Zijuan Zhang, Uri Laserson, Alberto Ciccia, Natalya Pavlova, George Church, Wei Zhang, Santosh Kesari and Stephen J Elledge doi:10.1038/nbt.2539 A library of in vitro translated human proteins tethered to their encoding mRNAs is used for unbiased discovery of interactions with immobilized proteins, autoantibodies or small molecules. Articles Compartmentalization of metabolic pathways in yeast mitochondria improves the production of branched-chain alcohols   pp335 - 341 Jose L Avalos, Gerald R Fink and Gregory Stephanopoulos doi:10.1038/nbt.2509 Relocation of metabolic pathways to yeast mitochondria can increase production levels compared with expression of the same pathways in the cytoplasm. See also: News and Views by DeLoache & Dueber Deciphering molecular circuits from genetic variation underlying transcriptional responsiveness to stimuli   pp342 - 349 Irit Gat-Viks, Nicolas Chevrier, Roni Wilentzik, Thomas Eisenhaure, Raktima Raychowdhury, Yael Steuerman, Alex K Shalek, Nir Hacohen, Ido Amit and Aviv Regev doi:10.1038/nbt.2519 A computational pipeline identifies genetic variants that affect transcriptional responses to stimuli, and uses this information to refine molecular circuits. Letters Efficient and specific gene knockdown by small interfering RNAs produced in bacteria   pp350 - 356 Linfeng Huang, Jingmin Jin, Padraig Deighan, Evgeny Kiner, Larry McReynolds and Judy Lieberman doi:10.1038/nbt.2537 Bacteria expressing a plant siRNA-binding protein produce potent, specific and nonimmunogenic siRNAs capable of knocking down target genes in mammalian cells. See also: News and Views by Blau & McManus Systematic identification of allosteric protein-metabolite interactions that control enzyme activity in vivo    pp357 - 361 Hannes Link, Karl Kochanowski and Uwe Sauer doi:10.1038/nbt.2489 Integrating metabolomics and computational modeling provides a method to identify allosteric enzyme-metabolite interactions, which have been inaccessible to systematic mapping. Careers and Recruitment Top Licensing lessons learned: if I knew then what I know now   pp362 - 363 Sadhana Chitale, Colm Lawler and Scott Macfarlane doi:10.1038/nbt.2551 Technology transfer professionals stress the importance of communication, staying informed and having flexible expectations. People People   p364 doi:10.1038/nbt.2558 Top Advertisement antibodypedia | nature invites you to participate in the "Annotate this Protein" contest! Submit independent data on one of our fifty-most-searched antigens for a chance to win a free subscription to your favorite Nature journal. 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